New Advances for In Situ Protein Identification by MALDI In-Source Decay FTMS Imaging

MALDI imaging mass spectrometry has proven to be effective for the discovery and the monitoring of disease-related proteins. With this technique a molecular analysis could be performed directly from tissue sections in the region of the diseased area. The use of in-source decay (ISD), allowing fast and reliable sequences assignments of proteins termini, has proven to be a crucial tool for proteins identification in solution and tissue slices. However, it is necessary to develop additional tools that allow unambiguous assignment of proteins sequences in complex tissue slices. The development of bioinformatic tools and the use of ultra-high mass resolution and high mass accuracy of Fourier transform ion-cyclotron (FTICR) mass spectrometry are ideal for this purpose. In this study, we show that FTICR mass spectrometry combined with data filtering with a software that subtracts matrix peaks aid protein identification.
All measurements were carried out on a SolariX FTMS (9.4 Tesla) equipped with a Dual Source with a smartbeamTMII laser (Bruker Daltonics). Mouse brain tissue slices of 14 µm thickness were rinsed to obtain optimal sensitivity and high-quality ions. Before matrix application, a spot of myelin was deposited near mouse brain. 1,5-Diaminionaphtalene was sprayed using an ImagePrep (Bruker Daltonics). Results were interpreted using BioToolsTM 3.2 in combination with MascotTM (Matrix Science) for ISD spectra and FlexImagingTM 3.0 for MALDI-ISD imaging experiments. Matrix peaks were subtracted using an in-house written Java code that sequentially scans all peak lists from acquired spectra against the DAN mass list. Then, another Java code allows to create 2D ion images at selected m/z ratios.
The studies were carried out by MALDI-ISD imaging to create interest on FTICR mass spectrometer for proteins identification in the field of biomarkers characterization. It is demonstrated that protein ISD leads to the same pattern of fragmentation observed during MALDI-TOF analyzes. Fragmentation generates cn- and zn-series ions of myelin in presence of DAN. The internal calibration of all the data provides a mass accuracy neighboring 2.5 ppm over the m/z range of interest (300-2500 Da) and a mass resolution of 70000 at m/z 400 Da. It allows the assignment of ISD fragments of proteins in the low mass range (m/z between 300 and 900) that is unambiguously validated by the “ISD signal” recorded from the spots of pure protein solution (myelin) near tissue slice. Moreover, the use of our software “cleans” MS imaging data by reducing/eliminating MALDI matrix peaks that are isobaric to an analyte peak.

Novel aspect

This study evidences the main input of FTICR mass spectrometer for pathologies diagnosis based on biomarkers localization and identification by MALDI-ISD imaging.